Name: construction and systematical symmetric studies of a series of supramolecular clusters with binary or ternary ammonium triphenylacetates
Uploaded: 2016-02-15T13:00:00.000+00:00
Duration: 6 min 35 s
Description: Watch this Scientific Journal Video about Construction and Systematical Symmetric Studies of a Series of Supramolecular Clusters with Binary or Ternary Ammonium Triphenylacetates at JoVE.com

This work was financially supported by Grant-in-Aid for Scienti&#64257;c Research B (24350072, 25288036) and Grant-in-Aid for Scienti&#64257;c Research on Innovative Areas (24108723) from MEXT and JSPS, Japan. T.S. acknowledges Grant-in-Aid for JSPS Fellows (25763), the GCOE Program of Osaka University and Grants for Excellent Graduate Schools, MEXT, Japan.

1.单晶制备组合主铵Triphenylacetates的<ol><li>制备的有机盐，伯铵triphenylacetates（图1a）。 <ol><li>溶解三苯基乙酸（TPAA，0.10克，0.35毫摩尔）和伯胺:N丁胺（N卜，2.5×10 -2克，0.35毫摩尔），异（isoBu，2.5×10 -2克，0.35毫摩尔），T丁胺（叔卜，2.5×10 -2克，0.35毫摩尔），或在TPAA 吨 -amylamine（叔上午，3.0×10 -2克，0.35毫摩尔），一起在甲醇（20毫升）:胺= 1:用于制备二元有机盐的摩尔比为1:1。 </li><li>在三元有机盐的情况下，溶解TPAA（0.10克，0.35毫摩尔）和两种伯胺:N卜（1.3×10 -2克，0.17毫摩尔） - T的卜（1.3×10 -2克，0.17毫摩尔），N卜（1.3×10 -2克，0.17毫摩尔） - T的上午（1.5×10 -2克，0.17毫摩尔），异卜（1.3×10 -2克，0.17毫摩尔） - T的卜（1.3×10 -2克，0.17毫摩尔），或isoBu（1.3×10 -2克，0.17毫摩尔） - T的上午（1.5×10 -2 g加速度 ，0.17毫摩尔），一起在甲醇（20毫升）的TPAA:胺-1:胺-2 = 2:1:1。 </li><li>蒸发所有通过旋转蒸发仪（40°C，200托）的解决方案，获得有机盐:TPAA-ñ卜，TPAA-isoBu，TPAA- 牛逼卜，TPAA- 牛逼上午，TPAA-ñ官僚牛逼卜，TPAA- ñ官僚ŧ上午，TPAA-isoBu- 牛逼卜和TPAA-isoBu-Ť上午。 </li></ol></li><li>准备超分子簇构成的单晶。 <ol><li>溶解每玻璃小瓶中在甲苯中作为非极性的良溶剂，其被选择是因为超分子簇在非极性环境优选构造的有机盐（5.0毫克）（0.30毫升）的。对于有机盐TPAA- 牛逼卜，TPAA- 牛逼上午，TPAA-isoBu- 牛逼卜和TPAA-isoBu- 牛逼上午，热甲苯上升ŤØ40℃溶解。 </li><li>添加己烷:0.5毫升，0.5毫升，0.5毫升，2毫升，2毫升，1毫升和0.5毫升，以TPAA-Ñ卜，TPAA-isoBu，TPAA- 吨上午，TPAA- n的有机盐的溶液官僚ŧ卜，TPAA-ñ卜- T的上午，TPAA-isoBu- 牛逼卜和TPAA-isoBu- 牛逼上午，分别作为不良溶剂以降低有机盐的溶解，除了有机盐溶液TPAA-ŧ卜。 </li><li>保持溶液稳定在在玻璃小瓶室温，在一天之内，得到单晶。 </li></ol></li><li>确认由傅立叶有机盐形成变换红外（FT-IR）光谱35,36。 <ol><li>在1混合用溴化钾（KBr压）的有机盐的单晶:100的重量比。 </li><li>用玛瑙研钵研磨该混合物，直到它变均匀粉末混合物。 </li><li>填补了一个圆模（直径5毫米）的粉末混合物，并用p粒料用压片机ressing它。 </li><li>把沉淀成的FT-IR光谱仪，并进行测量（累积数:16，分辨率1 -1）。 </li></ol></li></ol> 2.晶体学研究<ol><li>拿起从玻璃的有机盐TPAA- 吨上午的高质量单晶小瓶石蜡在玻璃板上。晶体看起来均匀的立体显微镜下，这意味着在晶体不是多晶，但单晶的组件，并具有0.3左右至1毫米的晶体尺寸无裂缝。 </li><li>把单晶上一个循环。 </li><li>设置在单晶X射线衍射设备单晶循环。 </li><li>选择一个准直仪:0.3，0.5，0.8，或1毫米，这取决于单个晶体的最大尺寸。 </li><li>启动单晶X射线衍射的预备测量使用单一C来自单晶收集X-射线衍射图案37,38rystal X射线衍射设备（辐射源:石墨单色Cu的Kαα（λ= 1.54187埃），曝光时间:30秒（确定基于所述晶体尺寸），检测器:例如成像板，晶体到检测器距离:127.40毫米，温度:213.1 K，帧数:3）。 </li><li>确定可能的晶体参数，并设定条件:曝光时间，X射线曝光的角度:ω，χ，φ，和帧数，对于基于上述预备测量的结果以下的测定。 </li><li>启动单晶X射线衍射的定期测量使用的条件下，单晶X-射线衍射设备来收集X射线衍射图案从单晶37,38（辐射源:石墨单色Cu的Kαα（λ= 1.54187埃），检测器:例如成像板，晶体到探测器DISTANCE:127.40毫米，温度:213.1 K）。 </li><li>通过直接的方法解决来自衍射图案的晶体结构，SIR2004 39或 SHELXS97 40，以及通过使用基于F 2的所有观察到的反射一个全矩阵最小二乘法修正。缩小所有各向异性位移参数的非氢原子，并放置的氢原子与相对于连接的非氢原子和未精制各向同性位移参数理想化位置。执行使用软件这些计算，如CrystalStructure 41。 </li><li>准直仪的尺寸，X射线预备测量和定期测量的曝光时间，和X射线曝光的角度:从步骤2.1至2.8与条件一些修改重复程序ω，χ，φ，和帧数，对有机盐的单晶:TPAA-ñ官僚牛逼卜，TPAA-ñ官僚&lt;EM&gt; T时许，TPAA-isoBu- 牛逼卜和TPAA-isoBu- 牛逼上午透露他们的晶体结构。 </li><li>检索有机盐的晶体结构:TPAA-ñ卜（refcode:MIBTOH）22，TPAA-isoBu（refcode:GIVFEX）24和 TPAA- 牛逼卜（refcode:GIVFIB）23日，使用软件剑桥结构数据库42，征服43，或申请表44。 </li><li>调查在通过使用软件如汞45-48和PYMOL 49计算机图形学的晶体结构的超分子集群;通过与以前归类那些（图1b）和三苯基作为Λ或Δ（图1a）的手性构象进行比较所得到的图案确定的在超分子簇氢键模式点群对称性。 </li><li>表征在每个晶体结构的超分子簇的多面体特征的有机盐。 <ol><li>删除所有的超分子簇的原子的除组分羧酸根阴离子和铵阳离子的碳和氮原子。 </li><li>使其中的原羧酸和铵阳离子由氢键连接的碳和氮原子之间的键。 </li><li>测量碳 - 碳和氮的氮原子，并且用于制备进一步键（5.3和4.1埃为碳 - 碳和氮 - 氮的距离，分别在这项研究中）设置的边界之间的距离。 </li><li>使碳 - 碳和氮的氮原子之间的进一步键，其中距离小于5.4和4.2埃，分别。 </li><li>确定产生的有机盐的多面体:TPAA-isoBu，TPAA- 牛逼卜，TPAA- 牛逼上午，TPAA-isoBu- 牛逼卜和TPAA-isoBu- 牛逼上午， 反式-bicapped八面体（T波），三角十二面体（TD），TD，TD和TD分别由considerin克旋转轴线 （C 3或C 2），以及所述多面体的边数。 </li><li>进行其他债券向所得的有机盐的多面体:TPAA-Ñ卜，TPAA-ÑBU- 吨卜和TPAA-ÑBU- 吨上午，通过考虑在超分子簇两侧，对称元素，以及分子间的相互作用的数因为他们有理想的人少面:TD，T波和四方反棱柱（SA）。 </li><li>通过做两个除了债券，由于其C 2对称性和14原债券确定TPAA-ñ卜盐Sa的多面体。确定TPAA-ÑBU- 吨卜和TPAA-ÑBU- 吨上午作为TD基于它们的 C 2对称性和超分子簇周围的三苯甲基的"带"的有机盐的其它多面体。即，在三元有机盐的超分子簇的三苯基团形成4;带"通过啮合他们的三苯基环和所述多面体TD具有侧连接4酸（ 图1c（ⅱ）），这意味着它们具有类似的结构特征。 </li></ol></li></ol>

The authors have nothing to disclose.

一系列封闭的氢键网络的超分子簇的成功构建和使用TPAA，其中有一个三苯甲基，及各类与伯胺的组合的有机盐手性的观点和多面体特征表征。在该方法中，关键的步骤是引入具有从非极性溶剂中的分子和反离子组成的有机盐膨松三苯甲基和重结晶的分子。这是因为，超分子簇具有一个倒胶束结构，即，离子氢键和疏水烃是内，外，分别。因此，该超分子簇是稳定的，在非极性环境中被选择性地构...

超分子是有趣和重要的研究目标，因为其独特的功能，如建筑超分子结构的，离子和/或分子，以及手性分离的感测，使用柔性非共价键1-11来自它们的分子识别能力。在分子认可，超分子组装的对称性是最重要的因素之一。尽管重要性，但仍然难以与由于在数量和种类的组件以及角度和非共价键的距离灵活性所需的对称性设计超分子。 基于系统化的研究超分子及其部件的对称性之间的相关性的澄清，是实现所需的超分子结构有用的策略。为了这个目的，超分子簇被选定为研究的目标，因为它们是由部件的数量有限的d为评估的理论12-14。然而，与金属配合物，有的构建超分子簇由于非共价键的稳定性低对维持超分子结构15,16的报告的数量有限。这个低稳定性也成为在获得一系列具有同种结构的超分子组装的问题。在这项研究中，有机盐，这是最稳健的非共价键17-20的一个电荷辅助氢键，主要用于构造特定超分子组装优先21-32。它还值得注意的是有机盐是由酸和碱，并且因此许多种有机盐仅仅通过酸和碱的不同组合的混合很容易获得。尤其，有机盐是对系统的研究中是有用，因为与各种抗衡离子的特定成分的组合产生相同类型supramo的lecular组件。因此，能够以比较根据各种抗衡离子的超分子组装的结构上的差异。 在以前的作品，超分子与0维（0-D）中，一维（1-D）和二维（2-D）由伯铵羧酸氢键网络被确认，并从手性的观点来看，其特征32。这些多维超分子是分层的水晶设计27重要的研究目标，以及利用其维度的应用。另外，氢键网络的表征将得到约生物分子的，因为所有的氨基酸的作用的重要知识有铵和羧酸基团。提供指引，以获得这些超分子分别使他们在应用进一步的机会。在这些超分子，建设的超分子簇以0-D-氢键网络是relativelŸ困难，表现在统计研究，28。然而，澄清的因素为构成超分子簇后，将它们有选择地构成，得到21-25,32一系列超分子簇。这些作品使人们有可能在超分子簇进行系统化对称的研究，阐明了超分子簇的依赖分量对称特性。为了这个目的，伯铵triphenylacetates的超分子簇具有有趣的特点，那就是，其拓扑多种氢键网络24,32，这将反映其对称的功能，以及作为组分三苯甲基的手性构象（图1a和1b）中 。这里方法论构建一系列使用伯铵triphenylacetates超分子簇和用于表征超分子簇的对称特征是魔trated。对于超分子簇的结构键引入从非极性溶剂的有机盐的笨重三苯甲基的和重结晶。二元和三元伯铵triphenylacetates被用于超分子簇的结构制备。从氢键网络24,32三苯甲基33,34，形貌（构象），和分子安排octacoordinated多面体12（图1c）的类似物拓扑观点考虑晶体学研究揭示了超分子簇的依赖分量对称特性25。

<table><tbody><tr><td>Triphenylacetic acid</td><td>Aldrich</td><td>T81205-10G</td><td></td></tr><tr><td>&lt;em&gt;n&lt;/em&gt;-Butylamine</td><td>TCI</td><td>B0707</td><td></td></tr><tr><td>Isobutylamine</td><td>TCI</td><td>I0095</td><td></td></tr><tr><td>&lt;em&gt;tert&lt;/em&gt;-Butylamine</td><td>TCI</td><td>B0709</td><td></td></tr><tr><td>&lt;em&gt;tert&lt;/em&gt;-Amylamine</td><td>TCI</td><td>A1002</td><td></td></tr><tr><td>Methanol</td><td>Wako</td><td>131-01826</td><td>hazardous substance</td></tr><tr><td>Toluene</td><td>Wako</td><td>204-01866</td><td>hazardous substance</td></tr><tr><td>Hexane</td><td>Wako</td><td>085-00416</td><td></td></tr><tr><td>KBr</td><td>Wako</td><td>165-17111</td><td></td></tr></tbody></table>

construction and systematical symmetric studies of a series of supramolecular clusters with binary or ternary ammonium triphenylacetates

在纳米或亚纳米级集群功能显著取决于不仅种类及其部件，而且安排，或对称，其组成部分。因此，在群集的安排已被精确地表征，特别是对金属配合物。与此相反，在有机分子组成的超分子簇分子安排表征限于少数病例。这是因为，超分子簇，尤其是获得了一系列超分子簇的结构，是困难的，由于非共价键的稳定性低比较共价键。从这个观点出发，有机盐利用是最有用的策略之一。一系列的超分子可以通过与各种抗衡离子的特定有机分子的组合来构造。尤其，伯铵羧酸盐是适合作为超分子因为各种羧酸的典型例子和伯胺是市售的，而且很容易改变其组合。以前，有人证实，使用各种伯胺的伯铵triphenylacetates具体构造超分子簇，这是由四个铵和四个triphenylacetates通过电荷辅助氢键组装时，在从非极性溶剂得到的结晶。这项研究表明超分子集群作为一种战略来进行系统性研究对称澄清在超分子的分子安排和种类及其组件的数量之间的相关性的具体构造的应用。与triphenylacetates构成二进制的盐和一种伯铵的，triphenylacetates组成三元有机盐和两种铵的相同的方式构造的超分子簇，得到与部件的各种种类和数量的一系列超分子簇的。

TPAA和伯胺的有机盐形成分别通过FT-IR测量的证实。有机盐的晶体结构经单晶X-射线衍射测定进行分析。其结果是，同种的超分子簇，这是由四个铵和四个triphenylacetates通过电荷辅助氢键（图1a）的，是在所有的有机盐的单晶确认种类和数量而不管成分铵（表1， 图2）。这一结果适用于系统性对称性研究，以澄清相关组件对称品种超分子...

Watch this Scientific Journal Video about Construction and Systematical Symmetric Studies of a Series of Supramolecular Clusters with Binary or Ternary Ammonium Triphenylacetates at JoVE.com

Construction and Systematical Symmetric Studies of a Series of Supramolecular Clusters with Binary or Ternary Ammonium Triphenylacetates

This article describes construction of a series of hydrogen-bonding supramolecular clusters in crystals using primary ammonium triphenylacetates, which are recrystallized from non-polar solvents. This selective construction of the supramolecular clusters leads to effective systematical symmetric studies about a correlation between the supramolecular clusters and their components.

建筑和超分子集群与二元或三元铵Triphenylacetates一系列的体制性对称研究

Functions of clusters in nano or sub-nano scale significantly depend on not only kinds of their components but also arrangements, or symmetry, of their ...

construction-systematical-symmetric-studies-series-supramolecular

Universidad de Cartagena UDEC

Research

JoVE Journal

Chemistry

8.0K 次观看.  Osaka University. This article describes construction of a series of hydrogen-bonding supramolecular clusters in crystals using primary ammonium triphenylacetates, which are recrystallized from non-polar solvents. This selective construction of the supramolecular clusters leads to effective systematical symmetric studies about a correlation between the supramolecular clusters and their components.

视频: Construction and Systematical Symmetric Studies of a Series of Supramolecular Clusters with Binary or Ternary Ammonium Triphenylacetates

Controlling the Size, Shape and Stability of Supramolecular Polymers in Water

For aqueous based supramolecular polymers, the simultaneous control over shape, size and stability is very difficult1. At the same time, the ability to do so is highly important in view of a number of applications in functional soft matter including electronics, biomedical engineering, and sensors. In the past, successful strategies to control the size and shape of supramolecular polymers typically focused on the use of templates2,3, end cappers4 or selective solvent techniques5. 
Here we disclose a strategy based on self-assembling discotic amphiphiles that leads to the control over stack length and shape of ordered, chiral columnar aggregates. By balancing electrostatic repulsive interactions on the hydrophilic rim and attractive non-covalent forces within the hydrophobic core of the polymerizing building block, we manage to create small and discrete spherical objects6,7. Increasing the salt concentration to screen the charges induces a sphere-to-rod transition. Intriguingly, this transition is expressed in an increase of cooperativity in the temperature-dependent self-assembly mechanism, and more stable aggregates are obtained. 
For our study we select a benzene-1,3,5-tricarboxamide (BTA) core connected to a hydrophilic metal chelate via a hydrophobic, fluorinated L-phenylalanine based spacer (Scheme 1). The metal chelate selected is a Gd(III)-DTPA complex that contains two overall remaining charges per complex and necessarily two counter ions. The one-dimensional growth of the aggregate is directed by &pi;-&pi; stacking and intermolecular hydrogen bonding. However, the electrostatic, repulsive forces that arise from the charges on the Gd(III)-DTPA complex start limiting the one-dimensional growth of the BTA-based discotic once a certain size is reached. At millimolar concentrations the formed aggregate has a spherical shape and a diameter of around 5 nm as inferred from 1H-NMR spectroscopy, small angle X-ray scattering, and cryogenic transmission electron microscopy (cryo-TEM). The strength of the electrostatic repulsive interactions between molecules can be reduced by increasing the salt concentration of the buffered solutions. This screening of the charges induces a transition from spherical aggregates into elongated rods with a length &gt; 25 nm. Cryo-TEM allows to visualise the changes in shape and size. In addition, CD spectroscopy permits to derive the mechanistic details of the self-assembly processes before and after the addition of salt. Importantly, the cooperativity -a key feature that dictates the physical properties of the produced supramolecular polymers- increases dramatically upon screening the electrostatic interactions. This increase in cooperativity results in a significant increase in the molecular weight of the formed supramolecular polymers in water.

The goal of this experiment is to determine and control the size, shape and stability of self-assembled discotic amphiphiles in water. For aqueous based supramolecular polymers such level of control is very difficult. We apply a strategy using both repulsive and attractive interactions. The experimental techniques applied to characterize this system are broadly applicable.

控制的大小，形状和稳定性超分子聚合物在水

For aqueous based supramolecular polymers, the simultaneous control over shape, size and stability is very difficult1. At the same time, the ability to do ...

科研

工程学

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities1,2. Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils3-8. A large variety of these peptides is commercially available.
This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a &#34;beads on a string&#34;-like structure by this process.9 The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

This paper describes the formation of highly ordered peptide-based structures by the spontaneous process of self-assembly. The method utilizes commercially available peptides and common lab equipment. This technique can be applied to a large variety of peptides and may lead to the discovery of new peptide-based assemblies.

生物分子有序结构由短肽的自组装形成

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control ...

化学

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13C/15N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Structures of supramolecular protein assemblies at atomic resolution are of high relevance because of their crucial roles in a variety of biological phenomena. Herein, we present a protocol to perform high-resolution structural studies on insoluble and non-crystalline macromolecular protein assemblies by magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS SSNMR).

固体核磁共振波谱法研究高分子组件的原子尺度结构

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the ...

生物化学

Synthesis and Characterization of Supramolecular Colloids

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical properties for applications in photonics, drug delivery and coating technology. Here we present a new family of colloidal building blocks, coined supramolecular colloids, whose self-assembly is controlled through surface-functionalization with a benzene-1,3,5-tricarboxamide (BTA) derived supramolecular moiety. Such BTAs interact via directional, strong, yet reversible hydrogen-bonds with other identical BTAs. Herein, a protocol is presented that describes how to couple these BTAs to colloids and how to quantify the number of coupling sites, which determines the multivalency of the supramolecular colloids. Light scattering measurements show that the refractive index of the colloids is almost matched with that of the solvent, which strongly reduces the van der Waals forces between the colloids. Before photo-activation, the colloids remain well dispersed, as the BTAs are equipped with a photo-labile group that blocks the formation of hydrogen-bonds. Controlled deprotection with UV-light activates the short-range hydrogen-bonds between the BTAs, which triggers the colloidal self-assembly. The evolution from the dispersed state to the clustered state is monitored by confocal microscopy. These results are further quantified by image analysis with simple routines using ImageJ and Matlab. This merger of supramolecular chemistry and colloidal science offers a direct route towards light- and thermo-responsive colloidal assembly encoded in the surface-grafted monolayer.

A protocol for the synthesis and characterization of colloids coated with supramolecular moieties is described. These supramolecular colloids undergo self-assembly upon the activation of the hydrogen-bonds between the surface-anchored molecules by UV-light.

超分子胶体的合成与表征

Control over colloidal assembly is of utmost importance for the development of functional colloidal materials with tailored structural and mechanical ...

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Protein-protein interactions involving proteins with multiple globular domains present technical challenges for determining how such complexes form and how the domains are oriented/positioned. Here, a protocol with the potential for elucidating which specific domains mediate interactions in multicomponent system through ab initio modeling is described. A method for calculating solution structures of macromolecules and their assemblies is provided that involves integrating data from small angle X-ray scattering (SAXS), chromatography, and atomic resolution structures together in a hybrid approach. A specific example is that of the complex of full-length nidogen-1, which assembles extracellular matrix proteins and forms an extended, curved nanostructure. One of its globular domains attaches to laminin &#947;-1, which structures the basement membrane. This provides a basis for determining accurate structures of flexible multidomain protein complexes and is enabled by synchrotron sources coupled with automation robotics and size exclusion chromatography systems. This combination allows rapid analysis in which multiple oligomeric states are separated just prior to SAXS data collection. The analysis yields information on the radius of gyration, particle dimension, molecular shape and interdomain pairing. The protocol for generating 3D models of complexes by fitting high-resolution structures of the component proteins is also given.

Here, we present how Small Angle X-Ray Scattering (SAXS) can be utilized to obtain information on low-resolution envelopes representing the macromolecular structures. When used in conjunction with high-resolution structural techniques such as X-Ray Crystallography and Nuclear Magnetic Resonance, SAXS can provide detailed insights into multidomain proteins and macromolecular complexes in-solution.

小角度 x 射线散射溶液中大分子的结构研究

Protein-protein interactions involving proteins with multiple globular domains present technical challenges for determining how such complexes form and ...

Synthesis and Characterization of 1,2-Dithiolane Modified Self-Assembling Peptides

This report focuses on the synthesis of an N-terminus 1,2-dithiolane modified self-assembling peptide and the characterization of the resulting self-assembled supramolecular structures. The synthetic route takes advantage of solid-phase peptide synthesis with the on-resin coupling of the dithiolane precursor molecule, 3-(acetylthio)-2-(acetylthiomethyl)propanoic acid, and the microwave-assisted thioacetate deprotection of the peptide N-terminus before final cleavage from the resin to yield the 1,2-dithiolane modified peptide. After the high-performance liquid chromatography (HPLC) purification of the 1,2-dithiolane peptide, derived from the nucleating core of the A&#946; peptide associated with Alzheimer&#39;s disease, the peptide is shown to self-assemble into cross-&#946; amyloid fibers. Protocols to characterize the amyloid fibers by Fourier-transform infrared spectroscopy (FT-IR), circular dichroism spectroscopy (CD) and transmission electron microscopy (TEM) are presented. The methods of N-terminal modification with a 1,2-dithiolane moiety to well-characterized self-assembling peptides can now be explored as model systems to develop post-assembly modification strategies and explore dynamic covalent chemistry on supramolecular peptide nanofiber surfaces.

A protocol for the synthesis of a 1,2-dithiolane modified peptide and the characterization of the supramolecular structures resulting from the peptide self-assembly.

12-Dithiolane 改性自组装肽的合成与表征

This report focuses on the synthesis of an N-terminus 1,2-dithiolane modified self-assembling peptide and the characterization of the resulting ...

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

The M42 aminopeptidases form functionally active complexes made of 12 subunits. Their assembly process appears to be regulated by their metal ion cofactors triggering a dimer-dodecamer transition. Upon metal ion binding, several structural modifications occur in the active site and at the interaction interface, shaping dimers to promote the self-assembly. To observe such modifications, stable oligomers must be isolated prior to structural study. Reported here is a method that allows the purification of stable dodecamers and dimers of TmPep1050, an M42 aminopeptidase of T. maritima, and their structure determination by X-ray crystallography. Dimers were prepared from dodecamers by removing metal ions with a chelating agent. Without their&#160;cofactor, dodecamers became less stable and were fully dissociated upon heating. The oligomeric structures were solved by the straightforward molecular replacement approach. To illustrate the methodology, the structure of a TmPep1050 variant, totally impaired in metal ion binding, is presented showing no further breakdown of dimers to monomers.

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

This protocol has been developed to study the dimer-dodecamer transition of TmPep1050, an M42 aminopeptidase, at the structural level. It is a straightforward pipeline starting from protein purification to X-ray data processing. Crystallogenesis, data set indexation, and molecular replacement have been emphasized through a case of study, TmPep1050H60A H307A variant.

X射线晶体学研究热木体马里蒂玛M42氨基肽TmPep1050的寡聚态过渡

The M42 aminopeptidases form functionally active complexes made of 12 subunits. Their assembly process appears to be regulated by their metal ion ...

Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

This protocol presents the use of Lewis acidic multi-role reagents to circumvent kinetic trapping observed during the self-assembly of information-encoded oligomeric strands mediated by paired dynamic covalent interactions in a manner mimicking the thermal cycling commonly employed for the self-assembly of complementary nucleic acid sequences. Primary amine monomers bearing aldehyde and amine pendant moieties are functionalized with orthogonal protecting groups for use as dynamic covalent reactant pairs. Using a modified automated peptide synthesizer, the primary amine monomers are encoded into oligo(peptoid) strands through solid-phase submonomer synthesis. Upon purification by high-performance liquid chromatography (HPLC) and characterization by electrospray ionization mass spectrometry (ESI-MS), sequence-specific oligomers are subjected to high-loading of a Lewis acidic rare-earth metal triflate which both deprotects the aldehyde moieties and affects the reactant pair equilibrium such that strands completely dissociate. Subsequently, a fraction of the Lewis acid is extracted, enabling annealing of complementary sequence-specific strands to form information-encoded molecular ladders characterized by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). The simple procedure outlined in this report circumvents kinetic traps commonly experienced in the field of dynamic covalent assembly and serves as a platform for the future design of robust, complex architectures.

A protocol is presented for the synthesis of information-encoded peptoid oligomers and for the sequence-directed self-assembly of these peptoids into molecular ladders using amines and aldehydes as dynamic covalent reactant pairs and Lewis acidic rare-earth metal triflates as multi-role reagents.

信息承载Peptoids及其序列定向动态共价自组装的合成

This protocol presents the use of Lewis acidic multi-role reagents to circumvent kinetic trapping observed during the self-assembly of information-encoded ...

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

The computational study of the formation and growth of atmospheric aerosols requires an accurate Gibbs free energy surface, which can be obtained from gas phase electronic structure and vibrational frequency calculations. These quantities are valid for those atmospheric clusters whose geometries correspond to a minimum on their potential energy surfaces. The Gibbs free energy of the minimum energy structure can be used to predict atmospheric concentrations of the cluster under a variety of conditions such as temperature and pressure. We present a computationally inexpensive procedure built on a genetic algorithm-based configurational sampling followed by a series of increasingly accurate screening calculations. The procedure starts by generating and evolving the geometries of a large set of configurations using semi-empirical models then refines the resulting unique structures at a series of high-level ab initio levels of theory. Finally, thermodynamic corrections are computed for the resulting set of minimum-energy structures and used to compute the Gibbs free energies of formation, equilibrium constants, and atmospheric concentrations. We present the application of this procedure to the study of hydrated glycine clusters under ambient conditions.

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

The atmospheric concentrations of weakly bound molecular clusters can be computed from the thermochemical properties of low energy structures found through a multi-step configurational sampling methodology utilizing a genetic algorithm and semi-empirical and ab initio quantum chemistry.

来自甲流热化学分子簇的大气浓度计算

The computational study of the formation and growth of atmospheric aerosols requires an accurate Gibbs free energy surface, which can be obtained from gas ...

Thermochemical Studies of Ni(II) and Zn(II) Ternary Complexes Using Ion Mobility-Mass Spectrometry

This article describes an experimental protocol using electrospray-ion mobility-mass spectrometry (ES-IM-MS) and energy-resolved threshold collision-induced dissociation (TCID) to measure the thermochemistry of the dissociation of negatively-charged [amb+M(II)+NTA]- ternary complexes into two product channels: [amb+M(II)] + NTA or [NTA+M(II)]-&#160;+ amb, where M = Zn or Ni and NTA is nitrilotriacetic acid. The complexes contain one of the alternative metal binding (amb) heptapeptides with the primary structures acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 or acetyl-Asp1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7, where the amino acids&#39; Aa1,2,6,7 positions are the potential metal-binding sites. Geometry-optimized stationary states of the ternary complexes and their products were selected from quantum chemistry calculations (presently the PM6 semi-empirical Hamiltonian) by comparing their electronic energies and their collision cross-sections (CCS) to those measured by ES-IM-MS. From the PM6 frequency calculations, the molecular parameters of the ternary complex and its products model the energy-dependent intensities of the two product channels using a competitive TCID method to determine the threshold energies of the reactions that relate to the 0 K enthalpies of dissociation (&#916;H0). Statistical mechanics thermal and entropy corrections using the PM6 rotational and vibrational frequencies provide the 298 K enthalpies of dissociation (&#916;H298). These methods describe an EI-IM-MS routine that can determine thermochemistry and equilibrium constants for a range of ternary metal ion complexes.

Thermochemical Studies of NiII and ZnII Ternary Complexes Using Ion Mobility-Mass Spectrometry

This article describes an experimental protocol using electrospray-ion mobility-mass spectrometry, semi-empirical quantum calculations, and energy-resolved threshold collision-induced dissociation to measure the relative thermochemistry of the dissociation of related ternary metal complexes.